The purpose of this project is to implement and to further develop the methods of molecular dynamics, stochastic dynamics, Monte Carlo, hydrodynamics and computer graphics to investigate the solution structures of peptides, proteins, nucleic acids and lipid bilayers. The project thus involves questions of both methodology and modeling. This past year the methodological part of the research principally involved: (i) the use of Langevin dynamics (LD) simulations to accelerate the isomerization rates of peptides; (ii) a comparison of LD simulations of a symmetric molecule in a Matier-Saupe potential with approximate analytic solutions of the Smoluchowski and Fokker-Planck equations; (iii) refinement of a force field to be used in molecular dynamics (MD)simulations of lipid bilayers; (iv) Monte Carlo generations of lipid configurations in a mean field; (v) a comparison of MD simulations of liquid butane using different constant temperature and pressure algorithms. Modeling projects included: (i) prediction of the hydration level of DNA from hydrodynamic calculations; (ii) determination of structure of a TT mismatch from molecular dynamics simulation of d(CGCGATTCGCG); (iii) inclusion of bilayer (molecular) properties into a model of synexin mediated membrane fusion; (iv) determination of digalactose structure, both in solution and bound to an antibody, using NMR data as a restraint on conformational search.
